Melatonin is an ancient molecule present in unicellular organisms at the very early moment of life. Initially identified as a secretory product of the pineal gland in mammals and in other species, it was considered a hormone related to reproduction. The evidence that melatonin is produced in many organs and tissues of the body, reaching concentrations higher than in the blood, support the multiplicity of the melatonin actions. The best-known actions of melatonin, currently supported by experimental and clinical data, include antioxidant and anti-inflammatory abilities, some of them involving genomic regulation of a series of enzymes. Besides, melatonin displays anticonvulsant and antiexcitotoxic properties. Most of the beneficial consequences resulting from melatonin administration may depend on its effects on mitochondrial physiology. The physiological effects of melatonin on normal mitochondria, its role to prevent mitochondrial impairment, energy failure, and apoptosis in oxidatively-damaged mitochondria, and the beneficial effects of the administration of melatonin in experimental and clinical diseases involving mitochondrial dysfunction and cell death, are revised.